Code: Select all
[16:29:36] - Warning: Could not delete all work unit files (2): Core file absent
[16:29:36] Trying to send all finished work units
[16:29:36] + No unsent completed units remaining.
[16:29:36] - Preparing to get new work unit...
[16:29:36] + Attempting to get work packet
[16:29:36] - Will indicate memory of 16003 MB
[16:29:36] - Connecting to assignment server
[16:29:36] Connecting to http://assign.stanford.edu:8080/
[16:29:37] Posted data.
[16:29:37] Initial: 43AB; - Successful: assigned to (171.67.108.24).
[16:29:37] + News From Folding@Home: Welcome to Folding@Home
[16:29:37] Loaded queue successfully.
[16:29:37] Connecting to http://171.67.108.24:8080/
[16:29:43] Posted data.
[16:29:43] Initial: 0000; - Receiving payload (expected size: 4856687)
[16:29:54] - Downloaded at ~431 kB/s
[16:29:54] - Averaged speed for that direction ~378 kB/s
[16:29:54] + Received work.
[16:29:54] Trying to send all finished work units
[16:29:54] + No unsent completed units remaining.
[16:29:54] + Closed connections
[16:29:54]
[16:29:54] + Processing work unit
[16:29:54] Core required: FahCore_a2.exe
[16:29:54] Core found.
[16:29:54] Working on queue slot 03 [February 21 16:29:54 UTC]
[16:29:54] + Working ...
[16:29:54] - Calling './mpiexec -np 4 -host 127.0.0.1 ./FahCore_a2.exe -dir work
/ -suffix 03 -checkpoint 15 -verbose -lifeline 4622 -version 624'
[16:29:54]
[16:29:54] *------------------------------*
[16:29:54] Folding@Home Gromacs SMP Core
[16:29:54] Version 2.04 (Thu Jan 29 16:43:57 PST 2009)
[16:29:54]
[16:29:54] Preparing to commence simulation
[16:29:54] - Ensuring status. Please wait.
[16:29:55] Called DecompressByteArray: compressed_data_size=4856175 data_size=24
043453, decompressed_data_size=24043453 diff=0
[16:29:55] - Digital signature verified
[16:29:55]
[16:29:55] Project: 2676 (Run 2, Clone 99, Gen 5)
[16:29:55]
[16:29:56] Assembly optimizations on if available.
[16:29:56] Entering M.D.
[16:30:05] (Run 2, Clone 99, Gen 5)
[16:30:05]
[16:30:05] Entering M.D.
NNODES=4, MYRANK=1, HOSTNAME=computenode
NNODES=4, MYRANK=3, HOSTNAME=computenode
NNODES=4, MYRANK=0, HOSTNAME=computenode
NNODES=4, MYRANK=2, HOSTNAME=computenode
NODEID=0 argc=20
NODEID=1 argc=20
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 4.0.3_pre (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
:-) mdrun (-:
Reading file work/wudata_03.tpr, VERSION 3.3.99_development_20070618 (single pre
cision)
NODEID=2 argc=20
NODEID=3 argc=20
Note: tpx file_version 48, software version 58
NOTE: The tpr file used for this simulation is in an old format, for less memory
usage and possibly more performance create a new tpr file with an up to date ve
rsion of grompp
Making 1D domain decomposition 1 x 1 x 4
starting mdrun '23121 system in water'
1500000 steps, 3000.0 ps (continuing from step 1250000, 2500.0 ps).
[16:47:36] Completed 5000 out of 250000 steps (2%)
[16:56:18] Completed 7500 out of 250000 steps (3%)
[17:05:01] Completed 10000 out of 250000 steps (4%)
[17:13:48] Completed 12500 out of 250000 steps (5%)
[17:22:36] Completed 15000 out of 250000 steps (6%)
[17:31:20] Completed 17500 out of 250000 steps (7%)
[17:40:07] Completed 20000 out of 250000 steps (8%)
[17:44:41] - Autosending finished units... [February 21 17:44:41 UTC]
[17:44:41] Trying to send all finished work units
[17:44:41] + No unsent completed units remaining.
[17:44:41] - Autosend completed
[17:48:56] Completed 22500 out of 250000 steps (9%)
[17:57:43] Completed 25000 out of 250000 steps (10%)
[18:06:29] Completed 27500 out of 250000 steps (11%)
[18:15:16] Completed 30000 out of 250000 steps (12%)
[18:24:04] Completed 32500 out of 250000 steps (13%)
[18:32:51] Completed 35000 out of 250000 steps (14%)
[18:41:36] Completed 37500 out of 250000 steps (15%)
[18:50:19] Completed 40000 out of 250000 steps (16%)
[18:59:04] Completed 42500 out of 250000 steps (17%)
[19:07:50] Completed 45000 out of 250000 steps (18%)
[19:16:33] Completed 47500 out of 250000 steps (19%)
[19:25:15] Completed 50000 out of 250000 steps (20%)
[19:34:02] Completed 52500 out of 250000 steps (21%)
[19:42:50] Completed 55000 out of 250000 steps (22%)
[19:51:36] Completed 57500 out of 250000 steps (23%)
[20:00:18] Completed 60000 out of 250000 steps (24%)
[20:09:01] Completed 62500 out of 250000 steps (25%)
[20:17:44] Completed 65000 out of 250000 steps (26%)
[20:26:26] Completed 67500 out of 250000 steps (27%)
[20:35:11] Completed 70000 out of 250000 steps (28%)
[20:43:55] Completed 72500 out of 250000 steps (29%)
[20:52:39] Completed 75000 out of 250000 steps (30%)
[21:01:22] Completed 77500 out of 250000 steps (31%)
[21:10:05] Completed 80000 out of 250000 steps (32%)
[21:18:50] Completed 82500 out of 250000 steps (33%)
[21:27:36] Completed 85000 out of 250000 steps (34%)
[21:36:22] Completed 87500 out of 250000 steps (35%)
[21:45:08] Completed 90000 out of 250000 steps (36%)
[21:53:53] Completed 92500 out of 250000 steps (37%)
[22:02:36] Completed 95000 out of 250000 steps (38%)
[22:11:18] Completed 97500 out of 250000 steps (39%)
[22:20:00] Completed 100000 out of 250000 steps (40%)
[22:28:42] Completed 102500 out of 250000 steps (41%)
[22:37:25] Completed 105000 out of 250000 steps (42%)
[22:46:09] Completed 107500 out of 250000 steps (43%)
[22:54:53] Completed 110000 out of 250000 steps (44%)
[23:03:40] Completed 112500 out of 250000 steps (45%)
[23:12:24] Completed 115000 out of 250000 steps (46%)
[23:21:08] Completed 117500 out of 250000 steps (47%)
[23:29:52] Completed 120000 out of 250000 steps (48%)
[23:38:38] Completed 122500 out of 250000 steps (49%)
[23:44:41] - Autosending finished units... [February 21 23:44:41 UTC]
[23:44:41] Trying to send all finished work units
[23:44:41] + No unsent completed units remaining.
[23:44:41] - Autosend completed
[23:47:24] Completed 125000 out of 250000 steps (50%)
[23:56:09] Completed 127500 out of 250000 steps (51%)
[00:04:54] Completed 130000 out of 250000 steps (52%)
[00:13:39] Completed 132500 out of 250000 steps (53%)
[00:22:26] Completed 135000 out of 250000 steps (54%)
[00:31:12] Completed 137500 out of 250000 steps (55%)
[00:39:58] Completed 140000 out of 250000 steps (56%)
[00:48:43] Completed 142500 out of 250000 steps (57%)
[00:57:27] Completed 145000 out of 250000 steps (58%)
[01:06:11] Completed 147500 out of 250000 steps (59%)
t = 2797.540 ps: Water molecule starting at atom 140947 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
[01:10:37]
[01:10:37] Folding@home Core Shutdown: INTERRUPTED
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 102) - process 0
[cli_1]: aborting job:
Fatal error in MPI_Sendrecv: Error message texts are not available
[cli_2]: aborting job:
Fatal error in MPI_Sendrecv: Error message texts are not available
[0]0:Return code = 102
[0]1:Return code = 1
[0]2:Return code = 1
[0]3:Return code = 0, signaled with Segmentation fault
[01:10:41] CoreStatus = 66 (102)
[01:10:41] + Shutdown requested by user. Exiting.***** Got a SIGTERM signal (15)
[01:10:41] Killing all core threads
Folding@Home Client Shutdown.
restarting client...